A script to make molecular dynamics (MD) datasets for neural networks from given LAMMPS trajectories automatically.
Project description
MDDatasetBuilder
MDDatasetBuilder is a script to build molecular dynamics (MD) datasets for neural networks from given LAMMPS trajectories automatically.
Author: Jinzhe Zeng
Email: jzzeng@stu.ecnu.edu.cn
Installation
pip install git+https://github.com/njzjz/mddatasetbuilder
Simple example
A LAMMPS dump file should be prepared. A LAMMPS bond file can be added for the addition information.
datasetbuilder -d dump.ch4 -b bonds.reaxc.ch4_new -a C H O -n ch4 -i 25
Then you can calculate generated Gaussian files:
qmcalc -d dataset_ch4_GJf/000
qmcalc -d dataset_ch4_GJf/001
Next, prepare DeePMD datas and use DeePMD-kit to train a model.
preparedeepmd -p dataset_ch4_GJf -a C H O
cd train && dp train train.json
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mddatasetbuilder-1.2.23.tar.gz
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